I just committed a fix for this to the repository. You can give it
a try once r3714 makes it to the compiled builds. The fix itself is
from Huw Jenkins, who also figured out a work-around: The problem only
occurs when the 3' nucleotide is a C, so just mutate the 3' terminal
nucleotide to anything other than a C, add a terminal nucleotide, and
then mutate it back to a C.
- Kevin
On 10/24/2011 11:09 AM, Francis E Reyes wrote:
> This seems to still be a problem for me. Adding a nucleotide to the 5' end it works fine, but adding to the 3' end gives me the following error:
>
>
> ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: -1 mol_base_is_purine: -1 std_base_is_pyrimidine: 0 std_base_is_purine: 1 mol_res_name: C std_base_name: A .
>
>
> Thanks!
>
> F
>
> On Aug 16, 2011, at 2:21 PM, Kevin Keating wrote:
>
>> I think I've fixed the problem for adding RNA nucleotides. One of the internal Coot functions wasn't fully updated with the new residue names (i.e A and C instead of Ar and Cr). Try out 0.7-pre-1 revision 3628 when it gets packaged for OS X and let me know if it works. Paul, should I back-port the fix to the 0.6.2 branch? It's no extra effort, but I wasn't sure if you wanted to completely freeze that branch.
>>
>> Also, as long as the subject of RNA has come up, I wanted to throw in a shameless plug for RCrane (http://pylelab.org/software/#rcrane). It's a Coot plugin that partially automates the building of RNA in maps of up to ~4 A resolution. I just released a new version of it last week (version 0.7), and I'd love to hear any feedback on it.
>>
>> - Kevin
>>
>>
>> On 8/16/2011 5:01 AM, Huw Jenkins wrote:
>>> Hi,
>>>
>>> Yet another reply to one of my own posts! Some more information though.
>>>
>>> I've now hacked the coot.info in fink and compiled the latest pre-release so I'm now running:
>>>
>>> 0.7-pre-1 (revision 3627) [with guile 1.8.8 embedded] [with python 2.7.2 embedded]
>>>
>>> The library was still the old version so I replaced /sw64/share/coot/lib with the directory from coot-0.7-pre-1-revision-3627-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz
>>>
>>> If I build DNA using the ideal DNA/RNA builder I can add nucleotides on to either end no problem. If I build RNA I get:
>>>
>>> ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: 1 mol_base_is_purine: 0 std_base_is_pyrimidine: -1 std_base_is_purine: -1 mol_res_name: U std_base_name: A
>>>
>>> Also if I mutate to Thymine using simple mutate C7 is missing (as reported a few days ago).
>>>
>>> Hopefully that'll help finding out what the problem is...
>>>
>>>
>>> Huw
>>> --
>>> Dr Huw Jenkins
>>> Astbury Centre for Structural Molecular Biology
>>> University of Leeds
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